# Pymol

Visualize, analyze, and render protein and molecular structures using PyMOL.

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill pymol -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill pymol -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill pymol -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill pymol -g -a gemini-cli -y`

## Description

Visualize, analyze, and render protein and molecular structures using PyMOL. Use when the user wants to create images of protein structures, perform structural alignments or superposition, measure distances or contacts, highlight binding sites or active site residues, color by B-factor/pLDDT, or analyze protein-ligand interactions. Do not use for docking, molecular dynamics, or sequence-only analysis.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# PyMOL

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If .licenses/pymol_LICENSE.txt does not already exist
    in the workspace root directory then (1) prominently notify the user to
    check the license at https://www.pymol.org/, then (2) create the file
    recording the notification text and timestamp.

## Overview

All PyMOL commands run on the host via `uv` with OSMesa software rendering, no
GPU, display, or X server is needed. Structure files must be downloaded to the
host before running PyMOL.

**Do NOT use when:**

-   The user wants to run AlphaFold predictions.
-   The user wants docking or molecular dynamics simulations.
-   The user only has a sequence and no structure file, fetch the structure
    first. Check if any other installed skills can retrieve structures from the
    PDB or AlphaFold Database before proceeding.

## Setup (Agent Instructions)

Ensure that `uv` is installed on the host system. The PyMOL scripts use PEP 0723
headers to declare their dependencies, and `uv run` will automatically handle
installing them (including `pymol-open-source-whl`) when the script is executed.

## Core Rules

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/pymol/SKILL.md